甘蓝型油菜MADS-box基因家族的鉴定与系统进化分析

doi:10.11983/CBB16244

摘要/Abstract

摘要： MADS-box基因家族参与调控开花时间、花器官分化、根系生长、分生组织分化、子房和配子发育、果实膨大及衰老等植物生长发育的重要过程。基于甘蓝型油菜(Brassica napus)基因组测序数据, 利用生物信息学方法对甘蓝型油菜MADS-box基因家族进行鉴定和注释及基因结构与系统进化分析。结果显示, 在甘蓝型油菜中鉴定出307个MADS-box基因家族成员, 根据进化关系可将其分为两大类型, I型(M-type)包含α、β、γ三个亚家族, II型(MIKC-type)包括MIKC^C和MIKC*两个亚家族, MIKC^C可进一步分为13个小类; 甘蓝型油菜A基因组染色体上分布的MADS-box基因多于C基因组。在基因结构上, MIKC-type亚家族基因序列普遍比M-type长且含有较多的外显子; M-type亚家族蛋白序列中的motif数量为2-5个, MIKC-type亚家族蛋白序列中平均含有7个motif。拟南芥(Arabidopsis thaliana)与甘蓝型油菜MADS-box基因共线性分析结果显示, 全基因组复制事件对MADS-box基因家族尤其是MIKC亚家族的扩张起重要作用; MIKC亚家族基因在进化过程中受到的选择压力约为M-type的2倍, 这表明MIKC-type亚家族在进化过程中被选择性保留。

关键词: 甘蓝型油菜, MADS-box, 基因结构, 进化, 共线性

Abstract: The MADS-box gene family is involved in many processes during plant growth and development, such as flowering time, floral organ differentiation, root growth, meristem differentiation, ovary and gamete development, fruit enlargement and senescence. In this study, we used rape (Brassica napus) genome sequencing data with bioinformatics methods to identify and annotate the MADS-box genes. Rape contains 307 members of MADS-box gene family. According to the evolutionary relationships, these genes can be divided into two subfamilies: I-type, also known as M-type, containing three subclades, α, β, and γ; II type, also known as MIKC-type containing two subclades, MIKC^C and MIKC*. MIKC^C can be further divided into 13 groups. The number of MADS-box genes is greater in the A than C subgenome chromosome of B. napus. For the gene structure, the sequence is longer for MIKC-type than M-type genes and contains more exons. The number of motifs in M-type genes is about 2-5, and MIKC-type genes contain an average of 7 motifs. Synteny analysis revealed that whole-genome duplication played a major role in the expansion of the BnaMADS gene family, especially the MIKC-type subfamily. The selection pressure of the MIKC-type subfamily was about 2 times that for the M-type, which resulted in the selective preservation of MIKC-type subfamily genes during evolution.

Key words: Brassica napus, MADS-box, gene structure, evolution, synteny

高虎虎, 张云霄, 胡胜武, 郭媛. 甘蓝型油菜MADS-box基因家族的鉴定与系统进化分析. 植物学报, 2017, 52(6): 699-712.

Gao Huhu, Zhang Yunxiao, Hu Shengwu, Guo Yuan. Genome-wide Survey and Phylogenetic Analysis of MADS-box Gene Family in Brassica napus. Chinese Bulletin of Botany, 2017, 52(6): 699-712.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB16244

https://www.chinbullbotany.com/CN/Y2017/V52/I6/699

图/表 9

图1 甘蓝型油菜、拟南芥和水稻的MADS-box基因系统发育分析(A) M-type; (B) MIKC-type

Figure 1 Phylogenetic analysis of rapeseed, Arabidopsis and rice MADS-box genes(A) M-type; (B) MIKC-type

图2 甘蓝型油菜MADS-box基因在染色体上的分布

Figure 2 Chromosomal location of MADS-box genes in Brassica napus

图3 甘蓝型油菜MADS-box基因在染色体上分布的统计

Figure 3 Statistics of MADS-box genes in chromosome of Brassica napus

表1 甘蓝型油菜MADS-box基因在亚基因组上的分布

Table 1 Distribution of MADS-box genes in subgenome of Brassica napus

Subgenome	M-type	MIKC-type	Total
A	55	85	140
C	52	77	129

图4 甘蓝型油菜MADS-box基因家族的motif结构(A) MIKCC亚家族; (B) MIKC*亚家族;(C) M-type亚家族

Figure 4 Motif patterns of different MADS-box gene families in Brassica napus(A) MIKCC subfamily; (B) MIKC* subfamily; (C) M-type subfamily

图5 与拟南芥共线性的MADS-box基因在甘蓝型油菜染色体上的分布

Figure 5 Distribution of MADS-box genes synteny with Arabidopsis thaliana in Brassica napus

图6 甘蓝型油菜与拟南芥MADS-box基因的共线性关系

Figure 6 Syntenic relationship of MADS-box genes between Arabidopsis thaliana and Brassica napus

图7 拟南芥MADS-box基因在甘蓝型油菜中的拷贝数

Figure 7 Copy number of Arabidopsis thaliana MADS-box genes in Brassica napus

表2 甘蓝型油菜MADS-box基因亚家族的选择压力

Table 2 Select pressure of MADS-box gene subfamily in Brassica napus

Subfamily	Arabidopsis	Brassica napus	Average copy number	Average Ka/Ks
Subfamily	thaliana	Brassica napus	Average copy number	Average Ka/Ks
M-type	20	34	1.7	0.43
MIKC-type	29	95	3.27	0.22

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